Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A6 F1 I0 R1	2892	75.3	5698161	66.1%	3766484	59.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,571,371	T→C	32.1%	intergenic (+139/‑1640)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,571,371	0	T	C	32.1%	223.9 / 157.4	190	intergenic (+139/‑1640)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (46/83); new base C (32/29); total (78/112)
Fisher's exact test for biased strand distribution p-value = 3.96e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 203 total aligned reads displayed.

GATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTC  >  minE/2571307‑2571441

gatgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                                                  <  1:1022779/71‑1 (MQ=255)

 atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATc                                                                   >  1:3425292/1‑71 (MQ=255)

   gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                                                                  <  1:3671395/68‑1 (MQ=255)

    tttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTc                                                               >  1:5093691/2‑71 (MQ=255)

     ttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCt                                                              >  1:1490904/1‑71 (MQ=255)

       ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                                                            <  1:4212067/70‑1 (MQ=255)

        ttccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt                                                             <  1:1754179/67‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:327799/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:2989061/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:4726710/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:5635651/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:529762/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                                            <  1:2759612/68‑1 (MQ=255)

         tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                                                            <  1:4254032/68‑1 (MQ=255)

           cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                                                          <  1:5031128/69‑1 (MQ=255)

           cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                                                         >  1:1524999/1‑71 (MQ=255)

           cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                                                         >  1:4842888/1‑71 (MQ=255)

           cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                                                         <  1:116806/71‑1 (MQ=255)

            tttAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTc                                                         <  1:475903/69‑1 (MQ=255)

              tAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGcc                                                     >  1:837254/1‑71 (MQ=255)

              tAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGGTCTGcc                                                     >  1:5014420/1‑71 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                                                                     >  1:4814237/1‑56 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                                                                     >  1:2221760/1‑56 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTgt                                                      >  1:5697330/1‑70 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                                                      >  1:5528958/1‑71 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                                                      >  1:2674080/1‑71 (MQ=255)

              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc                                                      >  1:2356605/1‑71 (MQ=255)

               aaTATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTgat                                                          >  1:3672967/1‑64 (MQ=255)

                atatTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCg                                                    <  1:1877765/70‑1 (MQ=255)

                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                                                                   >  1:4038816/1‑52 (MQ=255)

                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                                                        <  1:2512567/63‑1 (MQ=255)

                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                                                        <  1:1716614/63‑1 (MQ=255)

                     cATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                              >  1:1549294/1‑71 (MQ=255)

                      agcaTGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc                                                         >  1:5207379/4‑60 (MQ=255)

                      aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATg                                             <  1:4985725/71‑1 (MQ=255)

                       ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                                                                     <  1:4250179/46‑1 (MQ=255)

                       ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                                                                     <  1:398453/46‑1 (MQ=255)

                       ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt                                                          <  1:4167997/57‑1 (MQ=255)

                          tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:4295897/53‑1 (MQ=255)

                          tGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                                                            <  1:380857/53‑1 (MQ=255)

                            ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACta                                       <  1:1616543/71‑1 (MQ=255)

                            ttAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACt                                        <  1:3411049/70‑1 (MQ=255)

                             taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCt                                                              >  1:479064/1‑47 (MQ=255)

                             taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt                                                        >  1:3661204/1‑53 (MQ=255)

                             taataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTg                                                       >  1:4344942/1‑54 (MQ=255)

                               ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGt                                                           <  1:4440026/48‑1 (MQ=255)

                               ataaGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                     >  1:2060905/1‑70 (MQ=255)

                                      c‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCa                                                  >  1:5361385/1‑50 (MQ=255)

                                      c‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                              <  1:3511341/70‑1 (MQ=255)

                                      c‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                              <  1:5097885/70‑1 (MQ=255)

                                        t‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                              <  1:774512/69‑1 (MQ=255)

                                        t‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                              <  1:3932380/69‑1 (MQ=255)

                                          ggATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                                                            >  1:1598337/1‑38 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                              >  1:1469927/1‑51 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt                                              >  1:1823475/1‑51 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtc                              <  1:5436525/67‑1 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga                            <  1:2161337/69‑1 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga                            <  1:4143204/69‑1 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCga                            <  1:4149641/69‑1 (MQ=255)

                                           gATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGACGCAGGATGAGACTATACATCGTCgag                           <  1:3829152/70‑1 (MQ=255)

                                             tGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                 <  1:3844992/46‑1 (MQ=255)

                                             tGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACa                                   <  1:4685267/60‑1 (MQ=255)

                                             tGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACa                                   <  1:940354/60‑1 (MQ=255)

                                              gAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg                       >  1:463623/1‑71 (MQ=255)

                                              gAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCg                       >  1:1537116/1‑71 (MQ=255)

                                               aGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATga                                            <  1:1982580/49‑1 (MQ=255)

                                                gtgtGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCa                     <  1:227182/71‑1 (MQ=255)

                                                   tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                 <  1:5117893/40‑1 (MQ=255)

                                                   tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                 <  1:3201858/40‑1 (MQ=255)

                                                   tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatg                  <  1:1268388/71‑1 (MQ=255)

                                                   tgCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatg                  <  1:4960781/71‑1 (MQ=255)

                                                     ctctCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgat                <  1:151787/71‑1 (MQ=255)

                                                     atctcATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACg                       <  1:1855778/63‑1 (MQ=255)

                                                     atctcATTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACg                       <  1:4993226/63‑1 (MQ=255)

                                                      tctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                     >  1:2847201/1‑49 (MQ=255)

                                                       ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                 <  1:1381712/36‑1 (MQ=255)

                                                       ctcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg                                                 <  1:1266480/36‑1 (MQ=255)

                                                       ctcATTAGATTTCTCATCCGTCTTGATCTGTCCGATGACCAGACTGTGCATTGTTGAGAACGCACtaatga              >  1:2317238/1‑71 (MQ=255)

                                                        tcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCgaga                          >  1:4175455/1‑58 (MQ=255)

                                                        tcATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga              >  1:4314960/1‑70 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                     >  1:1706652/1‑46 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACtata                                     >  1:1435367/1‑46 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgatg               <  1:3904393/68‑1 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgatg               <  1:1937277/68‑1 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGata            >  1:1951030/1‑71 (MQ=255)

                                                         cATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGata            >  1:2811266/1‑71 (MQ=255)

                                                          aTTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAAtgatga              <  1:552476/68‑1 (MQ=255)

                                                          aTTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGatat           <  1:3135749/71‑1 (MQ=255)

                                                          aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCActaatg               <  1:4527043/67‑1 (MQ=255)

                                                          aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACtaatgaca            <  1:4734283/70‑3 (MQ=255)

                                                          aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACtaatgaca            <  1:3093088/70‑3 (MQ=255)

                                                          aTTGGATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGacat           >  1:3556466/1‑71 (MQ=255)

                                                           ttGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCa                     <  1:1107040/60‑1 (MQ=255)

                                                           ttGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAat                   <  1:5173566/62‑1 (MQ=255)

                                                             ggATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAg        >  1:2577682/1‑71 (MQ=255)

                                                             ggATTTCTTATCCGTCTTGATCTGCCCGATGACCAGACTGTGCATTGTTGAGAACGCACTAATGACATGa         <  1:1182047/70‑1 (MQ=255)

                                                                 tttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACAtcgtcg                             <  1:1363715/46‑1 (MQ=255)

                                                                 tttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAatgatg               >  1:2172702/1‑60 (MQ=255)

                                                                  ttttATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAgttgtt   >  1:622813/1‑71 (MQ=255)

                                                                   tttATCGGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCaa                    >  1:731348/1‑53 (MQ=255)

GATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATGAGACTATACATCGTCGAGATCGCAATGATGATATGAGTTGTTC  >  minE/2571307‑2571441

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A